Artifacts After pruning Unet CNN
Did you retrain the network after pruning the weights?

If not, 1) the bubbles are probably appearing because of that, and 2) you definitely should retrain your network.

Did you prune output features only or weights inside the network also?

The standard procedure is to retrain the network after pruning, and the best results can be achieved with iterative pruning: you prune small part of weights (the loss of accyracy is inevitable here), then retrain to get the accuracy back, and repeat until you won't be able to get the accuracy back to high level.

Here Pruning Convolutional Neural Networks for Resource Efficient Inference is an article about (among others) iterative pruning.